What Happened to Amelia Pond
by SingleDarkShade
Summary: Amelia Pond disappeared one day from Leadworth and Rory Williams has wondered ever since where his best friend was.
1. What Happened To Amelia Pond

Author's Note: A small random thought that came to me. I may add to it but for now it is a one-shot.

Enjoy.

* * *

Once upon a time in a small English village called Leadworth lived a young red haired Scottish girl named Amelia Pond who had a crack in her wall.

One night, when the voices coming from beyond it became too much to bear, she decided to ask for help from Santa - the only grown-up who had never let her down. To her surprise a Police Box crashed into the shed and a strange man appeared. He called himself the Doctor and told her of his magical box that had a library, a swimming pool and could travel in time. Then, after some interesting food choices, he fixed the crack in her wall.

Totally entranced by this strange man Amelia asked to travel with him so she could have adventures. To her amazement, because adults always told her she had to stay in stupid Leadworth, he told her she could but he would have to take his box away for five minutes to make sure it was safe.

She packed a case with everything she thought she would need, realising suddenly that she had to let her best friend know where she was going. Rory's mum had died a few months ago and his dad was still not well meaning he had to live with his gran, Amelia knew she couldn't just leave without letting him know where she'd gone or he'd worry. She quickly hid the message in their special secret hiding place so no one else would get it before she set her case down on the ground just where the box had been, sat on it waiting for the Doctor to come back.

No one would ever see little Amelia Pond again.

* * *

The van they'd hired made its way through the small streets of the quiet village. Leadworth was a picturesque little place with very little crime.

Patricia Kane, freshly graduated from teacher training and the village's newest Primary School teacher, sat in the passenger seat watching the houses pass by amazed by how perfect the place seemed to be.

Her research on the village had only found one thing to any real interest.

Ten years before a little girl had disappeared without a trace, typically from the house they were renting. It didn't bother her, despite her mother's concern of the history of the house; in fact Patricia was actually quite intrigued by the mystery.

"The 'Welcoming Committee' is here," Josh noted from the driver's seat as they drew close to the house.

Patricia chuckled at the resignation in his voice seeing Suzy Granger, the woman who had not only dealt with the renting of the house but was also part of the Village Council, standing waiting for them. They'd realised when looking for a place that living in a small village was going to be very different to living in the city.

x

"Suzy," Patricia greeted the woman the moment she slid out of the van.

"You've got a nice day to move in," Suzy smiled back, she handed over a small package, "This is all your keys with the code for the alarm."

Josh appeared at her side and nodded to the front garden, "Do we also get a security guard?"

"Oh," Suzy sighed as they all looked at the young man standing leaning against the large oak tree in the front garden staring at the shed. He had sandy hair and stood with his arms crossed, shoulders hunched sadness radiating from him, "That's Poor Rory. He won't be here for long."

Patricia turned to her confused, "Which means?"

"You were told the story of the little girl who lived here and disappeared ten years ago," Suzy said, continuing when they both nodded, "Well, Poor Rory was her best friend and it's the anniversary today."

"Do you think that's all one word or does he hyphenate?" Josh murmured in her ear while Suzy glanced back at their visitor again, getting an elbow in his ribs.

"I'll ask him to leave," Suzy said.

"No," Patricia stopped the other woman, "It's okay. Let him have his vigil."

Suzy smiled at her before she sighed, "Poor Rory, only a few months before Amelia disappeared he was in a car accident with his parents. His mother died and his father was so badly injured he lives with his grandmother. He's almost a fully qualified nurse which I must admit we all think was because of his losses."

"How old is he?" Josh asked interested, although a little stunned that they'd been given so much information on a stranger.

"Nineteen," Suzy replied, "He's a very intelligent boy. Threw himself into his studies after his losses, skipped several years of school and went to college early."

"Does he come here often?" Patricia asked.

Suzy shook her head, "No, only this day each year."

x

Rory leaned against the tree wondering where she was today.

Her message told him not to worry, that she was having adventures and maybe if her friend, the Doctor, agreed Rory could come on one too. No one believed him that the message he'd received had been from Amelia the night she disappeared. Instead they patted him on the head and murmured about the poor boy that lost his best friend just a few short months after losing his mum.

But Rory knew Amelia better than anyone and he knew that if she had told him she was going to have adventures then she was. Even as he grew and no longer looked at the world with the innocence of a child, Rory believed Amelia was having adventures with her magic Doctor.

Voices coming from behind him pulled Rory out of his musings and he grimaced when he saw the van, realising that the new tenants were moving in today. Seeing Suzy Granger standing there with two people he didn't recognise he winced but headed over to them.

"Sorry, I didn't realise you were moving in today," Rory apologised softly about to leave.

"How's your Gran, Rory?" Suzy asked before turning to the couple standing there, "She's a lovely woman, makes the best home-baked chocolate cakes for the fetes but has been a bit poorly."

"She's feeling better," Rory stated.

"You know," the man said suddenly, "I should start unpacking the van otherwise I won't get it back in time."

Rory was surprised when the man made a small head jerk to him but spoke up, "Do you want some help?"

"Great," the reply came and Rory followed on to the back of the van.

"Thanks for the rescue," Rory said softly.

"I'm Josh," he introduced himself, "I could see the look on your face when Suzy started giving us all the details. I take it privacy is something that happens elsewhere."

Rory nodded, "You learn to live with it."

"Or you could leave," Josh suggested as he started to pull out boxes.

Rory shrugged, "It's an idea. I'll take these inside."

"One question," Josh stopped him, "Is Poor Rory one word or do you hyphenate?"

Rory started to laugh, not sure why because it wasn't even funny but every time he looked at Josh he started again making the other man laugh as well.

* * *

Rory dropped onto the couch with a sigh, smiling when Patricia passed him a mug of tea, "Thanks."

"Bad day?" she asked, sitting on the chair and propping her legs up on the table.

Rory took a long drink of tea, "Long day. Where's Josh?"

"He'll be home soon," she replied, "He's bringing dinner."

Relaxing back and watching the movie Rory smiled slightly. Despite the hideous introduction they'd had, Patricia and Josh had become great friends to him. They were the only people in the village who didn't look at him like he was some charity case and he loved them for it.

He even found himself talking about Amelia every so often.

It was strange that somehow he'd found new friends in the house where his childhood friend had lived. He'd helped them move in then Josh had asked him to help assemble some furniture, which did not go as well as it should have but left the three of them in hysterical laughter. He'd then been asked to help paint some of the rooms and several months later Rory was a regular for dinner at least three times a week.

x

Patricia adored Rory.

He was very smart, supremely sarcastic when he wanted to be, extremely observant and very sweet. Josh was the eldest of four already so had just slotted Rory into the same category as his brothers. The younger man readily agreed to help them with anything for the house, although he would not go into the room that had been Amelia's bedroom. She realised that for the first time in a long time Rory had people who didn't think of him as 'Poor Rory', people he could spend time with who liked him but didn't think of him as some broken waif.

To her surprise, after a few months, he even spoke to them about Amelia. Neither said anything at his steadfast belief she was alive having adventures but they didn't treat him like an idiot either for the hope he carried it was true.

* * *

"No," Rory stated folding his arms across his chest decisively.

"Yes," Patricia told him, "You are coming and you going to enjoy yourself."

Rory frowned at her, "On a blind date with Josh's sister's friend from work?"

Josh chuckled holding his hands up defensively when his girlfriend and his friend both glared at him, "I'm not involved in this."

"It's your sister's friend," Rory threw at him.

Patricia sat at his side, "Okay, how about I make you a deal."

Rory grimaced but remained silent.

"You come for dinner and, if you're not enjoying yourself, I will let you use the 'working early in the morning' excuse to get out of there right after we eat," she told him.

Rory sighed in defeat, "Does it have to be tonight?"

Josh and Patricia shared a look before she rested a hand on his shoulder, "It's been eleven years, Rory. You are allowed to move on."

Anger filled Rory's eyes which faded when his two friends looked at him concerned, "I know it's stupid, I know she isn't going to magically appear one day but I..." he trailed off not sure how to voice his need to watch for her. He knew no one believed that Amelia was having adventures, he knew that it was an utterly ridiculous idea that he did but it was one he couldn't let go of.

"Come on," Josh said, "It'll be a laugh."

Sighing Rory gave in.

x

Jane was nice.

Rory was stunned to find he actually liked her and, to his surprise, she seemed to like him too. With a lot of pushing from Josh and Patricia he asked her out and they began dating. They were together for six months, Rory did his best but Jane wanted more from him than he was able to give her.

His grandmother needed his help, he'd been taken on full time at the hospital which gave him an erratic schedule and then there were his memories of Amelia. In the end she didn't like coming second to the memory of his childhood best friend and broke up with him.

Josh and Patricia tried a few more times to set him up but most only lasted a few dates. And then as the twelfth anniversary of Amelia's disappearance came around things became very strange.

* * *

Rory followed Dr Ramsden through the ward, wishing it had been one of the other doctors on because for some reason she didn't seem to like him. Something strange was going on, the patients in the coma ward were wandering about the village. He'd seen them, he had photographic evidence but no one would listen to him. It wasn't because he was just a nurse, it was because he was so much younger than everyone else. His twenty-first was in three days and he was worrying what Patricia and Josh had planned as they kept grinning at him whenever it was mentioned.

"So," Dr Ramsden demanded, "They all called out at once, that's what you're saying?"

Rory grimaced at the tone of her voice.

"All of them. All the coma patients?" she continued harshly, "You do understand that these people are all comatose, don't you? They can't speak."

"Yes, Doctor Ramsden," Rory replied.

"Then why are you wasting my time?" she snapped at him.

Rory winced before saying softly, "Because they called for you."

"Me?"

"Doctor," one of the patients called before Rory could reply, "Doctor. Doctor."

Rory looked at the woman standing across from him seeing the same confusion in her eyes that he felt as the other patients took up the call.

"Doctor. Doctor. Doctor. Doctor. Doctor."

After several minutes silence filled the ward again and Dr Ramsden checked the closest patient.

"I don't think they were even conscious," she said thoughtfully.

Rory knew it was probably a bad idea but he pushed on anyway, "Doctor Ramsden, there is another sort of funny thing."

"Yes, I know," she stated, "Doctor Carver told me about your conversation. We've been very patient with you, Rory. You're a good enough nurse, but for God's sake."

"I've seen them," Rory tried to get her to listen to him while he pulled out his phone to find the pictures.

She frowned at him, "These patients are under twenty four hour supervision. We know if their blood pressure changes. There is no possibility that you could have seen them wandering about the village. Why are you giving me your phone?"

"It's a camera too," he explained, relieved when she reached for it, her beeper sounded and she waved him away again.

"You need to take some time off, Rory," she told him, stopping him from arguing, "A lot of time off. Start now," he tried to protest once more, "Now."

x

Rory parked his car and dropped his head against the steering wheel. He'd sent a text to Patricia and Josh telling them what had happened, they were the only people in his life he could talk to because they were the only ones who didn't think of him as 'Poor Rory'.

Frustrated he decided to walk for a while, he really didn't want to explain to his gran why he was home from work early.

He was beginning to think about leaving Leadworth. There was very little keeping him here except the memory of a friend who had left twelve years ago and the grandmother who needed him. As he wandered the village green without thought Rory spotted one of the coma patients out with his dog. Pulling out his phone he was vaguely aware that the light seemed to be coming through a filter of some kind.

Rory jumped when his phone was snatched out his hands.

"The sun's going out," a strange man in a pin-striped suit that looked as though it had seen better days said, "And you're photographing a man and a dog. Why?"

"What?" Rory demanded confused.

"Man and dog. Why?" the man snapped, "Tell me now."

Rory shook himself and replied, "Because he can't be there. Because he's in a hospital, in a coma," bemused as the man said the words with him Rory nodded, "Yeah."

The man grinned at him, "Knew it. Multiform, you see? Disguise itself as anything, but it needs a life feed. A psychic link with a living but dormant mind."

"Who the hell are you?" Rory blurted out spinning as the coma patient began to bark instead of the dog.

"I'm the Doctor," the man replied absently before he confronted the strange image before them.

Rory was completely caught by how the man introduced himself that he barely noticed the alien spaceship, the explosions and the man turning to liquid before sliding down the drain.

"No TARDIS, no screwdriver, seventeen minutes," the man was muttering to himself, "Come on, think. Think!"

"You're the Doctor?" Rory demanded, pulling the other man out his mutterings, "As in Amelia's Doctor?"

The Doctor turned to him, "You know Amelia Pond?"

"Where is she?" Rory asked stunned, "Is she with you or did you leave her at your box?"

The Doctor stared at him confused, "What?"

"Amelia," Rory clarified, "I was her friend. If she's back I want to see her."

"What's your name?"

"I'm Rory," he introduced himself.

The Doctor took a breath, "I now have less than seventeen minutes to stop the aliens from blowing up your planet, Rory. Can we focus on that just now and then we'll talk about Amelia after the Earth is safe?"

Rory nodded, "Okay."

The Doctor pulled a phone out of his pocket, adding Rory's number to it and thrust it at Rory, "Get to the hospital. Get everyone out of that ward. Clear the whole floor. Phone me when you're done."

x

"Rory!"

He turned to Patricia as she came running towards him across the hospital car park, "You can't be here. Something..."

"The Police Box," she cut him off, "It's appeared in the garden."

Rory nodded, "I thought it might have."

She stared at him confused, similar to the look she gave him when he explained Amelia's farewell message before she asked, "How?"

"Because I just met the Doctor," he explained.

"What?!" she stared at him, "Is she with him?"

Rory winced, "I don't know because there are aliens trying to destroy the world and I have to help."

Patricia stared at him before shrugging, "So what do we need to do?"

He took a breath, "You get everyone out of the hospital while I check the ward."

x

Rory stared in amazement at the man, now dressed in clothes he'd stolen from the lockers, who had just called back aliens who were going to blow up the planet and told them off.

"Okay," the strange man turned to Rory, "Let's talk about Amelia."

Rory let out a laugh, "I always wondered if maybe it wasn't true but meeting you, seeing what you just did I can even believe the time travel."

The Doctor held up his hand, "Rory, where is Amelia?"

"She's with you," Rory said before frowning confused, "Isn't she?"

The Doctor shook his head, "Rory, I left Amelia less than half an hour ago. I meant to get back to her in five minutes but the TARDIS took a little longer than I expected."

Rory stared at him horrified, "But that means..."

"I'm sorry, Rory," the Doctor apologised, "I don't know where Amelia is."

Bile rose up in his throat as the weight of the words came crashing down on him, Amelia hadn't gone with the Doctor. She hadn't spent the past twelve years having adventures. Something bad had happened to her.

The world around him spun and he felt two arms catch him before he was set down to sit against the wall.

"It's okay," the Doctor said, "Deep breaths. We'll work this out?"

"How?" Rory demanded grabbing the other man by his jacket letting out a cry when something burned him.

The Doctor pulled out a key which was glowing, "I have to get back to the TARDIS and make sure she's fixed."

Nodding absently Rory forced himself to his feet and followed the strange man.

x

The blue Police Box sat just to one side of the shed and Rory stared in amazement to see it.

"So that's your magic blue box," Rory whispered folding his arms across his chest.

The Doctor nodded patting the side of it affectionately, "This is the TARDIS."

"Small," Rory noted.

"There's no need to be rude," the Doctor noted before shaking his head, "Alright, about Amelia. Tell me everything."

Rory shrugged, "There's not much to tell. She disappeared one night."

"How did you know about me?" the Doctor asked.

"She left me a message," he explained, "I found it the next morning in our secret place and I know it was new because there was nothing there when I'd left earlier that afternoon."

The Doctor frowned, "Okay, I need to see the message."

Rory nodded, "It's at home."

"You go get that," the Doctor told him, "I need to check the TARDIS is working. I'll meet you back here in an hour?"

"Okay," Rory replied.

Two days later Rory resigned himself to the fact the other man was not coming back.

* * *

A few months had passed since all the weirdness happened in Leadworth and the Doctor had saved the world, Patricia shook her head fondly finding Rory fast asleep in the chair beside the hospital bed, still in his scrubs. Checking the woman on the bed she smiled to see she was awake.

"Hi, Mrs Williams," Patricia said softly, "How are you feeling?"

"I'm fine, dear," June Williams replied weakly, "Just a little tired."

Patricia nodded, knowing she was much sicker than she would ever admit.

"Has that grandson of mine gone home?" June asked.

Patricia winced and moved out the way so she could see Rory unconscious in the chair, "I'll move him."

"I was so glad when he met you and Josh," June sighed softly, "He's such a good boy but I know he finds it hard to make new friends after losing Amelia."

Patricia smiled at the old woman, "Well, it's easy to like Rory."

"I worry what he'll do after I die," June whispered, "I know he's only staying here for me."

"You don't have to worry," Patricia assured her, "We'll look after him, I promise."

June caught Patricia's hand, "Thank you. Can you make him go home for me just now?"

Patricia nodded, "Of course I will."

x

Rory stared at the coffin feeling Patricia and Josh on either side of him as he said goodbye to his grandmother. He knew she was dying. He was a nurse, he'd seen it plenty of times but for some reason he hadn't been prepared for losing her. Rory was also trying not to let his anger for his father take over, anger that the man couldn't get over his issues to come to his mother's funeral.

It was now a year and a half since the Doctor had appeared and told him that he had no idea where Amelia was, where Rory had discovered something had happened to her and then the Doctor had disappeared again. Losing his gran had thrown Rory into a world where he had no idea what he was going to do now. It was only his two friends standing by his side that kept him going, that kept him from just curling onto a ball of misery while everyone gave him their condolences. Finally they left the cemetery and Rory was guided to the pub where a wake had been set up.

"I can't do this," Rory whispered when they reached the entrance, "I can't..."

Patricia gently rubbed his back, "It's okay. Josh will take you back to the house. You can stay with us as long as you need."

Rory hugged her grateful for her support before he let Josh lead him back to the car. He'd been staying with them since his grandmother had died, unable to go back to the home he'd grown up in since she was no longer there.

Exhausted by the day Rory undid his tie and pulled off his jacket discarding them unseen on sofa before he dropped to sit.

It was time to leave Leadworth.

* * *

"Final day at work," Josh noted when Rory walked into the kitchen, "How did it go?"

Rory shrugged, "It seemed like any other day but we had cake."

Patricia chuckled, "Bring any for us?"

"Like there was any left," Rory rolled his eyes before looking at the couple before him, "I never would have made it to this without you two. You know that. I'm so grateful to both of you for becoming my friends and giving me a place to stay for the past few months."

Patricia moved and wrapped him in her arms, "You're our family, Rory. You know that and we will always be here for you."

"Even if we hate you for the fact you're going to see the world while we're stuck here," Josh teased, laughing when his fiancé smacked his arm.

Rory chuckled, "Well at least we'll meet up in Spain in a few months for your wedding."

"Let's have dinner," Patricia said, "And we'll celebrate your last night with us before you go travelling."

"Pizza is on the way," Josh told them.

x

Rory grimaced feeling Patricia shake him awake while calling his name. His sleep fogged brain wondered what was going on wincing when she shook him again.

"Go away," he murmured burying his face into his pillow.

"Rory," Patricia called, "You need to wake up."

Batting her away he sighed, "Go annoy your fiancé if you can't sleep."

"The blue box is back," Patricia told him.

Rory jumped awake, running to the window he saw the TARDIS sitting there. Pushing on his trainers he ran out the door with Patricia just behind him.

"Rory," the Doctor greeted when he exited his ship, "Sorry, little later than I intended but the TARDIS just rebuilt herself so there's always going to be a few glitches."

Rory stared at him, "A little later?"

"What is it?" the Doctor looked up, "A couple of hours."

"Try a couple of years," Rory snapped at him.

The Doctor winced, "Oops."

"Oops?" Rory yelled, "That's all you have to say? Because I have spent over a decade wondering what happened to my friend and you appear possibly with answers then bugger off for a few more years."

"I am sorry, Rory," the Doctor told him sincerely, "But I'm here now and I want answers as much as you do."

Sighing Rory said, "Alright."

"Do you have the letter she left you?"

With a grimace Rory nodded, "I'll be back in a minute. Do not move."

"I promise," the Doctor replied.

x

Rory found Amelia's letter grabbing the rucksack sitting packed for his trip. Reaching the box again he thrust the paper at the man aware of Patricia standing at his side.

The Doctor studied the letter for several moments, licking the paper making Rory wince in disgust.

"Alright," the Doctor finally said, "I will use the traces of Amelia to do my best to find her."

"I'm coming," Rory told him.

The Doctor stared at him for a few minutes before nodding, "Alright. Let's go."

"I'm coming too," Patricia said stopping Rory from arguing, "You're not doing this alone."

Rory stared at her for a few seconds before shrugging, "Tell Josh you're coming so he doesn't worry."

Patricia patted his arm, "I'll be right back."

Rory waited until she entered the house before turning to the Doctor, "We're going now."

"You know I have a time machine," the Doctor noted, "I can get you both back ten minutes ago."

"Your track record so far doesn't fill me with confidence," Rory replied, "I won't let Josh spend years wondering when she'll come back. So we go without her."

Opening the door to the TARDIS the Doctor let Rory inside smiling slightly when he stalled seeing the large room there. Closing the door he quickly started the engines and taking them into a temporal orbit. He glanced over to where Rory stared around the massive room inside the small box. He dropped his bag and slowly took a few steps further inside.

"It's...It's..."

"I know," the Doctor grinned before becoming serious, "Alright, this might take some time but I promise you, Rory that we will find what happened to Amelia."  
Rory nodded.

The Doctor grinned, "Then let's get going."


	2. Searching

Author's Note: I have plans for more chapters

Enjoy.

* * *

Rory stomped back into the TARDIS, dripping wet and barely holding onto his temper.

"Okay," the Doctor said following him inside, "That didn't quite go the way I expected."

"Really?" Rory snapped, "It didn't quite go the way you expected?"

The Doctor frowned, "You seem to be a little upset, Rory."

"I almost drowned," Rory reminded him sharply, "Twice. In less than an hour."

"But you didn't," the Doctor replied, clapping him on the shoulder, "And we stopped an entire village from being destroyed."

Rory wiped his face with his hand, which didn't really help much as rivulets of water continued to fall from his hair, "We're meant to be looking for Amelia."

Bouncing up the stairs to the console the Doctor started the TARDIS moving, "And we are, Rory. The TARDIS just got a little side-tracked."

Jaw set in annoyance Rory followed him upstairs grabbing the rail when the TARDIS started moving.

"You should go and get changed before you catch a cold," the Doctor said absently as he moved around the console.

Deflating Rory headed to his room knowing he was dripping water behind him, but he'd fix that once he was dry again. He knew it was stupid, but he'd hoped that the Doctor would be able to just take him to Amelia instantly and the big question in his life would be answered.

x

The room he had in the TARDIS was amazing. It felt like home which in all honesty surprised him. He glanced at the two pictures he had on the bedside cabinet that he had packed, one of him with Patricia and Josh, the other of Amelia.

Guilt filled him that he'd left Patricia without saying anything, but he didn't want Josh to spend all his time wondering where his fiancé had disappeared to. He also missed them both and, as well as he got along with the Doctor, the Time Lord wasn't the same as his two friends.

Taking a shower Rory sighed in relief when he was warm, dry and wearing clean clothes once more. He headed back to the console room finding the Doctor still wandering around the console pushing buttons and pulling levers.

"Feel better?" the Time Lord asked.

Rory nodded, "Yes. Sorry I..."

"Not a problem," the Doctor cut him off.

"It is," Rory insisted, "I'm feeling guilty I left Patricia without saying anything."

The Doctor said nothing simply letting him speak.

"I walked away," Rory continued, "Because I didn't want her to leave Josh wondering where she was and when she was going to come home."

The Doctor looked at him thoughtfully for a moment before holding out his hand, "Give me your phone."

Confused Rory pulled out his mobile and handed it to the other man, "Why?"

After checking it over, the Doctor picked up the sonic, tapped some controls on it for a moment and aimed the sonic at the phone before passing it back to Rory, "Call her."

"What?"

"Universal roaming," he smiled, "You can keep in touch with them."

Surprised Rory called Patricia, holding it up to his ear to listen stunned when she answered.

"Hi, Patricia," he said softly.

"Rory?" surprise filled her voice, "Where are you?"

He smiled slightly happy to be talking to her, "I'm in the TARDIS with the Doctor. I wanted to apologise…"

"Wait," she cut him off, "Your phone works? I thought it was a Time Machine."

Rory chuckled, "The Doctor fixed it. You can call me if you need to now."

"That's good," she said, "So, how's your search going?"

"Not great yet," Rory sighed, "I'm sorry I just left, I just didn't want Josh to be left to wonder where you were."

"I know. Just be careful," Patricia told him, "And call us whenever you need to talk."

* * *

Rory sat on the roof of the house looking up at the stars as he listened to the songs of the villagers celebrating their harvest. In the centre of the circle he could see the little red-haired girl dancing. He turned when the Doctor appeared and took a seat at Rory's side.

"Are you alright?"

Rory sighed, "I actually thought for a moment we'd found her."

The Time Lord wrapped an arm around his friend's shoulders, hugging him close, "I know. So did I."

"We've been doing this for six months," Rory whispered, "I thought we'd find something by now. Even a trace of her but I think…."

"Rory?"

"I think I have to admit she's gone," Rory continued sadly, "It's something I should have accepted a long time ago."

The Doctor grimaced, "Are you sure about that? You're ready to go home?"

Rory's head came up, "I didn't say that."

"You still want to travel with me?" the Doctor asked with a grin.

"If you want me to," Rory replied, giving a slight smile, "I mean it can be mind-numbingly terrifying at times but then I see this," he motioned to the people in front of him, "And it's all worth it to know I helped save these people."

The Doctor clapped him on the shoulder, "Then let's get out of here."

With a smile Rory stood and they walked back to the TARDIS together.

x

The TARDIS was in flight and the Doctor mused over where to go next. Rory was sleeping but would be awake soon. Now that the young man had decided to travel just to travel, the Doctor had been trying to find fun destinations for him. Their last stop hadn't turned out to be all that fun but they helped a Starship about to crash get home safely.

He was still trying to find Amelia but not telling Rory that he was. Now he'd decided to stop the search, Rory had been quieter than before. The Doctor understood that Rory was coming to terms with his decision to stop searching for his childhood best friend. Hearing footsteps the Doctor turned and smiled at his companion who was wandering down the stairs pushing his fingers through his hair, "Morning, Rory. How are you feeling?"

"Like I ran a marathon I hadn't trained for," Rory replied with a slight smile before asking, "Where are we going?"

The Doctor grinned, "I thought we would go to the Moons of Algoria. It is a fantastic place to go for a party and they celebrate basically everything."

Rory grinned back and nodded, "Sounds like fun."

Before the Doctor could start them moving Rory's phone began to ring.

x

Rory gave an apologetic shrug to the Doctor as he pulled out his phone, smiling to see Patricia was calling him.

"Hi," he answered.

"Rory," Patricia said softly, "You need to come home."

Confused Rory put the phone on speaker, "Why?"

There was silence for a moment before she spoke again, "Are you able to see the news for here?"

Looking up at the Time Lord who nodded Rory replied, "Yes. What channel?"

"It doesn't matter," Patricia replied softly.

"Rory," the Doctor called making him turn to the viewscreen.

He stared at the headline on the screen before him, 'Fourteen-year-old mystery solved, Amelia Pond's body found.'

"…Leadworth over fourteen years ago," the newsreader said as the sound came up, "The body of Amelia Pond, who was seven years old when she disappeared, was found today in the garden of a house in Leadworth village as it was being dug up for renovations. Currently the cause of death is unknown. Amelia is survived by her aunt who moved away the year after the disappearance."

Rory let out a shaky breath, "Patricia, when did this happen?"

"Last week," she told him, "But it was this morning we found out who…you should come home. They've already organised the funeral for next week."

Staring at the phone Rory tried to speak again, every word getting stuck in his throat.

"We'll be there, Patricia," the Doctor said before he hung up. He rested an arm around Rory and moved him to sit, "Rory?"

Rory looked up at his friend sadness filling his voice, "Fifteen years and she was there all along," tears filled his eyes, "I wanted her to be out here somewhere having adventures. I wanted to find her but not like this."

The Doctor hugged him tightly, "I know, Rory. I know."

Rory dropped his head onto his friend's shoulder, giving in as he was rocked gently by the Time Lord whose own sadness at the news was palpable.

After several minutes Rory pulled back, "We should go."

The Doctor nodded and silently set the co-ordinates. They landed and Rory numbly followed the Doctor out the TARDIS. Patricia and Josh stood waiting at their door, enfolding him into a hug the moment he was within reach.

* * *

Rory walked slowly through the main street hoping to avoid the journalists who had invaded the village for the funeral. The service had been hell. Amelia's aunt had clung to his arm throughout the entire thing, which meant he had to be the strong one. Something he didn't feel.

The Doctor was somewhere, having stood at the back for the funeral but had promised he wouldn't leave until Rory was ready.

Taking a seat at the duck pond and stared at the water wishing things had been different, that he could have done something different.

"So," a female voice came from beside him as someone sat at his side, "I picked the wrong time to come visit family."

Rory turned slightly finding a woman with long black hair, pale skin and hazel eyes sitting at his side. She was beautiful, looked to be close in ages to him and Rory felt he should know her. Then again if she was visiting family, it was more than likely he did. Leadworth was not that big.

"Yes, you did," he replied softly.

"Did you know her?" she asked, before clarifying, "The girl who died."

Rory nodded sadly, "She was my best friend."

She rested her hand on his arm, "I'm sorry. This must be so hard for you."

"I guess it's closure," he whispered, not sure why he was telling her this.

Noise coming towards them made him look up and he grimaced realising the horde of journalists were about to find him. He'd managed to avoid every one of them all day because he did not want to tell his story or be shown as the pathetic childhood friend finally getting closure.

"Hey," the strange woman took his hand, "Come on, I know somewhere you can hide."

Not sure why, Rory let her pull him through the village. They ran along the back street towards the B&B near the edge of town, once there she tugged him inside and locked the door.

Rory let out a sigh of relief. He pulled out his phone to let Patricia and Josh know where he was, surprised when it was snatched out of his hand.

"What are you doing?" Rory demanded, trying to grab his phone back.

The woman pouted at him, "I thought we were having a nice conversation. Why do you want to talk to someone else?"

"I just don't want my friends to worry," Rory replied aware the door was locked, and he couldn't see any other way out of the room.

She tilted her head, "I thought I was your best friend, Rory. Why are you trying to leave me?"

"Wh…What are you talking about?" he took a step back, searching for an exit or a way to get to a phone.

Reaching up she pulled the black hair off her head, revealing it was a wig and a mass of red hair fell around her face. She threw the wig to one side and walked towards him. Rory backed away, wincing when he hit the wall. She rested her hands on his chest giving him a smile.

"Surely you recognise me now?" she whispered softly, "I thought you'd recognise me, Rory."

Rory stared at her confused but as he looked at the pale face, now framed with flame-red hair and the eyes looking into his, the impossible answer hit him.

"Amelia?" he breathed.

A grin covered her face, "I prefer to be called Amy now but…surprise."

"No," Rory shook his head, "But the funeral…they found…the funeral…"

Amy smiled at him, "I had to get you back here somehow, Rory."

He continued to stare at her, jerking his head away when she stroked his cheek.

"I thought you'd be happy to see me," Amy whispered with a slight pout, "I'm so happy to see you. You grew up cute. I didn't expect to find you so attractive when they told me our destiny."

Rory stared at her, "Our what?"

Amy smiled and her lips brushed against his quickly before she stepped away from him and touched her watch.

"We're going to save the universe," Amy told him intently, "From the biggest threat it's ever faced."

"Which is?"

Anger filled her eyes and steel filled her voice, "The Doctor."

x

Amy frowned, confused that Rory wasn't as happy to see her as she thought he'd be. It had been a long time since they'd seen one another but he had described himself as her best friend when they talked.

"What do you mean?" he asked softly taking a step forward as Amy moved to sit, "How is the Doctor a threat?"

Before she could speak the door burst open and three soldiers appeared, they grabbed Rory who tried to get away but within seconds he was on his knees, hands cuffed behind his back and a gag in his mouth.

"I thought we agreed you would find him and alert us before you spoke to him," Madam Kovarian noted with disapproval when she entered the building.

Amy shrugged, "I wanted to talk to him. He's still my Rory, even if he's been corrupted by the Doctor."

Leaning down, Kovarian grabbed Rory's chin tilting his face so he would look up at her, "Nothing appears special about you but then all we need is for you to do one thing." She nodded to the soldiers and two of them yanked him to his feet.

Amy could see fear in his eyes and wanted to assure him not to worry. They were doing something good and it was only because the Doctor had influenced him that they needed to take precautions.

"It's time to return to the ship, Amelia," Kovarian noted, "Let's go."

Amy nodded, retrieving the wig before she followed on. Not too happy at how Rory was being dragged along but he was fighting so much.

"Hey," a woman called suddenly, "Let him go."

Amy turned seeing the Doctor with a man and a woman she didn't recognise. The Doctor pointed his sonic device at Rory and the handcuffs unlocked. The moment he was released Rory slammed his shoulder into one of the guards. Taken by surprise they couldn't stop him as he ran towards the Doctor.

"Amy," Kovarian called, "Back to the ship now."

Rory stalled turning back and reaching out his hand to Amy, "Please," he whispered, "Come with me."

"Amy," Kovarian snapped again.

"Please," Rory said softly, "Don't leave again. Stay with me. Amelia…Amy…"

She stared at him, remembering her best friend who would follow her anywhere, looking at the man he had become.

His eyes pleading with her.

Unconsciously Amy's hand moved towards him. Their fingers touched and Amy gave a cry when she was pulled away by a soldier seeing the Doctor grab a hold of Rory to stop him chasing after her.

As she was dragged away, Amy stayed focussed on his face until the doors of the ship closed blocking him from view.

While Kovarian and the others started for the bridge, Amy slid to sit on the floor. She'd been raised to believe in her destiny, raised to know the Doctor was evil and with Rory she would be the one to stop him.

But now…

Rory wouldn't help someone bad, he couldn't.

And as she sat Amy began to wonder if what they were doing was right.


	3. Taking Chances

"Rory?" Patricia offered him the mug of tea, he took it silently, sadness covering his face. Crouching at his side she gently stroked his arm, "I know this is hard but she's alive, that's a good thing."

Taking a drink of his tea, Rory shrugged.

The Doctor, who had been standing in silence in one corner of the hall since they'd returned to the house, suddenly walked into the kitchen. He then turned and walked upstairs to what had been Amelia's bedroom before he ran back down to the garden.

"What are you doing?" Rory demanded when the other man finally stopped.

"Working through events," the Doctor replied before turning to Rory again. Reaching out to cup the younger man's cheek, he said, "I'm going to fix this. We're going to get her back."

Pulling back Rory demanded, "How?"

Hesitating, the Doctor finally admitted, "I'm not sure right now but," he caught Rory's arms again so the younger man would look up at him, "I will."

"Did they tell you what they wanted you for?" Josh asked thoughtfully.

Rory grimaced, "The woman said all they needed was for me to do one thing."

"That's concerning," Patricia mused, "Any ideas what she meant by that?"

Rory shook his head, "I need some time alone." As he started to walk away from them all three yelled his name. He paused and turned back, "I am going to my room in the TARDIS."

Patricia moved to his side, "We're just worried after what happened earlier."

"I know," he said softly, "But I need some time alone."

Without another word he walked to the blue box sitting beside the house and disappeared inside.

x

Patricia watched Rory leave before she turned to the man standing beside her, "Doctor, I know you've promised Rory that you'll find Amelia, but you have to protect him. Rory is blind when it comes to Amelia. She means the world to him and now he knows she's alive…" she sighed, "You need to protect him."

The Doctor gently nodded, "Always."

Josh grimaced, "If he lets you." At his fiancée's stern look, Josh shrugged, "You know Rory."

"Why don't you both head back inside," the Doctor suggested, "Be here to keep Rory from going off on his own. I need to look around the village for any clues where these people have gone."

"Doctor," Patricia called, "What if they come back?"

He shook his head, "They're after Rory. He's safe inside the TARDIS. If they come back, join him. She'll let you in."

The Doctor rested his hands on each of their arms, "I am going to protect you all, I promise. But I have to try to save Amelia."

With a nod he stalked away with determination. Patricia and Josh watched him leave, Josh wrapped his arm around her.

"Come on," he ushered her back inside, both hoping the Doctor was able to protect their friend.

x

Rory sat on his bed with his knees pulled up to his chest as he went through every second that he'd spent with Amelia…Amy. Trying to look for clues in their interaction, in case she'd given him any information that he could use to find her again.

Pushing himself off the bed he began to pace, hoping to clear his head because all he could think of was the look on her face when they pulled her away. He began to walk the corridors of the TARDIS, needing to get rid of the energy filling his body and found himself in the control room. Where a mobile phone sat on the console in front of him.

Rory began to wonder if she still had his phone, he didn't remember her putting it down after taking it from him. Picking up the phone he typed a quick message before tapping in his number and sending it.

Taking a seat on the stairs he waited, hoping she'd answer.

x

Amy dropped onto her bed in relief. Madam Kovarian had punished her for not obeying orders and talking to Rory instead of calling them.

But she'd seen him and couldn't resist talking to him. Then Amy started to remember how much she missed him.

Rory had been her best friend; he would almost always do whatever she wanted, and he was always there to listen when Aunt Sharon annoyed her. She remembered when Aunt Sharon had told her that he had been in a car accident with his mum and dad, how the cold fear that she would never see him again filled her. She'd cried learning that his mum had died, because Mrs Williams always been so nice.

Amy had hugged him tightly when she saw him a few days later, sitting in his room with him and talked for him because he didn't want to talk to anyone but her at that time.

She hadn't meant to leave him for so long, but in order for the plan Madam Kovarian developed to save the universe they had to be adults when they saw one another again.

And Amy had believed in it.

Seeing her jacket on the floor, Amy picked it up knowing she'd be punished for leaving it there, surprised at the weight. Searching the pockets, she found Rory's phone. Pushing the button, the screen lit up and she saw there was a message waiting for him. Wondering who was contacting him curiosity got the better of her.

 _Amy_ , it said, _Code is the day and month we first met_.

Smiling to herself, Amy entered in 0507, the 5th July. The first full day she'd been in Leadworth. To her joy, it unlocked the phone and Amy smiled.

Part of her knew she should tell Madam Kovarian that she had this, but she wanted to make sure he was alright first. Amy couldn't get the look on his face out of her mind, the pleading in his eyes for her to stay this time.

Opening the emails and messages, Amy frowned to see there were very few personnel ones. She didn't understand why he didn't have more friends because Rory was the best friend anyone could ever have.

Opening the pictures on the phone, she frowned. There some with the Doctor as well as the man and woman who had been with the Time Lord. Reaching the end, Amy smiled when she found one of her. It looked as though it was a picture of a photograph, but he kept a picture of her with him and warmth blossomed in Amy.

She bit her lip in thought. He'd wanted her to be able to unlock the phone meaning he wanted her to contact him.

Taking a breath, she typed:

 _I remember._

Sending the two words, she sat and watched the screen. Waiting. Hoping he'd contact her again. When the phone buzzed, she grabbed it.

 _Are you alright? Have they hurt you after today?_

Amy smiled at his concern.

 _I'm fine. Did the Doctor hurt you?_

 _Of course not. He's my friend. We've been trying to find you._

x

Rory sat on the stairs of the TARDIS relieved Amy still had his phone and had answered him. He was concerned that she thought the Doctor was not the good man he was and worried what the people who had taken her had done to make her believe this.

 _Where are you?_

He knew it was a long shot she'd tell him, but he needed to try.

 _I think about you every day_ , Amy's next message said ignoring his question, _I didn't want to leave you, but they told me it was for protection._

 _Protection from what?_

Rory watched the screen and waited for her to reply.

 _Do you forgive me for leaving?_

He sighed that she wouldn't answer his questions but if these people had programmed her to believe that the Doctor was bad then he had to be very careful.

 _Of course I do_ , he paused for a moment before asking, _Do you forgive me for not recognising you earlier?_

A few seconds later she replied, _Yes. I shouldn't have surprised you like that, but I was so excited to see you again._

 _I've been trying to find you,_ Rory typed back, _With the Doctor's help. I never forgot you and thought of you every day._

No answer came through for several minutes and Rory began to worry. Finally a message came through

 _Will you meet me? Just us, I promise._

Rory stared at her message. He wanted to tell her yes, he desperately wanted to, but he couldn't trust her. Could he?

 _Rory, please come and meet me._

Wrapping his arms around his knees, Rory debated with himself. He wanted to see her, to make sure she was alright and hopefully talk her into coming home. But after what happened he knew he had to be careful.

 _Meet me at the spot we would count clouds._

It was a bit obscure but only Amy and Rory would know where that was. Plus it meant he knew he could see if anyone followed her.

 _I'll see you in an hour._

* * *

Rory had never been that good at climbing trees as a kid. He'd fallen out one at the age of six, after Amelia had goaded him into climbing it, and broken his arm. Which led to him sitting in a hospital with Amelia holding his other hand, tears filling her eyes that he was hurt. However, since meeting the Doctor his climbing skills, along with running and computer abilities had grown exponentially. Which was why he'd chosen this spot to meet Amy.

Since they had been children the trees in the area had grown and there were several that he was able to hide in so he could watch to make sure there was no one following her.

Sneaking away hadn't been easy but Rory knew how to be move quietly so people didn't see him. Although he had brought the phone and had it set up ready to call for help if needed.

He spotted her easily, her long red hair streaming behind her as she ran through the field. Rory smiled to see that the little girl he had known was still in there somewhere.

Amy found their old spot at the big rock and took a seat, she leaned back on the flat surface and smiled as she lay in the sun.

Rory waited for about ten more minutes, watching Amy and ensuring that no one was waiting in the wings to try to grab him again.

Finally, feeling assured she'd come alone Rory climbed down and moved slowly to her.

"Amy," he said softly.

Her head came up and a bright smile covered her face, "Rory!"

Amy jumped up and ran to him, throwing her arms around him tightly to his surprise.

"You're okay?" Amy pulled back and started to check that he wasn't injured after what happened that morning.

"I told you I was," Rory smiled, he brushed her hair back and asked, "Are you?"

Amy nodded before she hugged him again. Rory closed his eyes and held her to him, sighing happy that he'd found her.

"I can't stay long," Amy spoke up after a few minutes, not moving from their embrace, "Madam Kovarian will be looking for me soon."

"You know you don't have to go back," Rory said, "You can stay with me," he winced when she pulled away, "Amy…"

"I can't," she whispered.

Rory took her face in his hands, "Yes, you can. You might not remember but I do. Amelia Pond who did nothing that anyone told her. Who took orders as suggestions," he smiled sweetly at her, "Who persuaded me to break rules."

A smile touched her lips, "You were always so nervy whenever we did something we weren't supposed to."

He nodded, "And then you were gone."

Sadly she looked away, stepping back to take a seat again.

"My best friend," Rory continued, sitting at her side, "Who promised she'd never leave me like my mum and dad did."

"Rory," she grabbed his hand, "I didn't want to leave you but…"

"But?" he demanded when she trailed off.

Amy sighed, leaning against his shoulder, "It used to be so clear. Until I saw you again. It doesn't make sense anymore."

Rory rests his head against hers whispering, "Then stay. Come back with me and forget whatever they told you. It's nonsense."

"I…"

"Trust me," Rory breathed turning her to look at him.

Amy nodded, wrapping her arms around him in a tight hug.

Holding her Rory knew he had his best friend back and, at that moment, nothing else mattered.


End file.
